Analysis of pairs of neurons (or partial neurons) that synapse onto one another
a reciprocal pair of neurons that synapse onto one another
Use the list_of_all_reciprocal_pairs.ipynb
notebook to list and analyze all the reciprocal synapses in the
volume. A special thank you to Wanwen Zeng at Stanford for
generating the dictionary code to generate the reciprocal synapse
list.
Use the reciprocal_pairs_neurons_with_soma_in_volume.ipynb
notebook to list and analyze all the reciprocal pairs of neurons
that have an identified soma within the Layer 2/3 volume.
Use the reciprocal_pairs_synapse_visualizer.ipynb
notebook to generate 2D and 3D visualizations (using matplotlib,
meshparty and vtk) of synapses for a desired set of reciprocal pairs.
Includes over a dozen example pairs.
The paired.csv
datatable contains all the reciprocal pairs (n = 1998/2 = 999) in
the entire volume, including all the partial processes as well.
The pairs_rm_v_g_na.csv
datatable contains the reciprocal pairs where both pairs have an
identified soma in the volume, filtering out vascular and glial cells
(because these are mis-segmented synapses anyway!), as well as filtering
out the partial proceses. This was generated using the 220309_cell_type_classification.csv
datatable. Confession: due to my novice pandas skills, I found
it more expedient to create the datatable in Excel using a simple
vlookup function.
Martinotti-bipolar reciprocal pair
The inhibitory Martinotti neuron makes two synapses onto another inhibitory bipolar neuron. In turn, the bipolar neuron makes eight synapses onto the Martinotti neuron. Closeup 3D views (using meshparty and vtk) and the original electron micrograph views (in Neuroglancer) of select synapses are shown as well.
3D rendering of Martinotti synapses onto a bipolar neuron using vtk visualizer
electron micrographs of Martinotti synapses onto the bipolar neuron
3D rendering of bipolar synapse onto a Martinotti neuron using vtk visualizer
electron micrographs of a bipolar neuron synapse onto the Martinotti neuron